Potential targets of VIVIPAROUS1/ABI3‐LIKE1 (VAL1) repression in developing Arabidopsis thaliana embryos

Abstract

These authors contributed equally to this work. SUMMARYDeveloping Arabidopsis seeds accumulate oils and seed storage proteins synthesized by the pathways of primary metabolism. Seed development and metabolism are positively regulated by transcription factors belonging to the LAFL (LEC1, AB13, FUSCA3 and LEC2) regulatory network. The VAL gene family encodes repressors of the seed maturation program in germinating seeds, although they are also expressed during seed maturation. The possible regulatory role of VAL1 in seed development has not been studied to date. Reverse genetics revealed that val1 mutant seeds accumulated elevated levels of proteins compared with the wild type, suggesting that VAL1 functions as a repressor of seed metabolism; however, in the absence of VAL1, the levels of metabolites, ABA, auxin and jasmonate derivatives did not change significantly in developing embryos. Two VAL1 splice variants were identified through RNA sequencing analysis: a full-length form and a truncated form lacking the plant homeodomain-like domain associated with epigenetic repression. None of the transcripts encoding the core LAFL network transcription factors were affected in val1 embryos. Instead, activation of VAL1 by FUSCA3 appears to result in the repression of a subset of seed maturation genes downstream of core LAFL regulators, as 39% of transcripts in the FUSCA3 regulon were derepressed in the val1 mutant. The LEC1 and LEC2 regulons also responded, but to a lesser extent. Additional 832 transcripts that were not LAFL targets were derepressed in val1 mutant embryos. These transcripts are candidate targets of VAL1, acting through epigenetic and/or transcriptional repression.

HSI2/VAL1 Silences AGL15 to Regulate the Developmental Transition from Seed Maturation to Vegetative Growth in Arabidopsis

“…Our ChIP results confirmed that a mutant form of HSI2 with a disrupted PHD domain fails to accumulate at the 5ʹ region of the AGL15 locus in vivo (Figure 6). Through RNA sequencing analysis, Schneider et al (2016) identified two HSI2 splice variants: a full-length form and a truncated form that lacks coding sequences for the PHD domain. Translation of the truncated HSI2 transcript would produce a protein variant, similar to HSL2 that contains intact B3, CW, and EAR motifs but lacks the PHD domain (Jia et al, 2014).…”

The Arabidopsis Polycomb Repressive Complex 1 (PRC1) Components AtBMI1A, B, and C Impact Gene Networks throughout All Stages of Plant Development

“…Interestingly, two VAL1 splice variants have been identified through RNA sequencing analysis: a full-length form and a truncated form lacking the plant homeodomain-like domain similar to VAL3, which also lacks the plant homeodomain-like domain (Schneider et al, 2016). It is possible that truncated VAL1 and VAL3 target this group of genes, explaining their lack of up-regulation in val1/2 mutants.…”

A Machine Learning Approach to Predict Gene Regulatory Networks in Seed Development in Arabidopsis

“…There are not many known negative regulators involved in seed development (Jia et al, 2013). One of these repressors is VIVIPAROUS1/ABI3-LIKE1 (VAL1), which is known to repress genes involved in the embryonic program (Schneider et al, 2016) and is also positively regulated by FUS3 (Wang and Perry, 2013). VAL1 was not differentially expressed above the cutoff (see Section Materials and Methods, above), so the VAL1 gene was absent from any clusters.…”

“…This data set contains the expression profiles of a total of 53,989 transcripts expressed in embryos of different ages represented by seven time points (7, 8, 10, 12, 13, 15, and 17 days after pollination (DAP) in three biological and four technical replicates; Schneider et al, 2016). Expression of these transcripts was normalized using fragments per kilobase of transcript per million mapped reads (FPKM).…”

“…The gene expression levels in FPKM was calculated by summing the FPKM expression values from all splice variants (transcripts originating from the same gene) for a given gene for each time point. Limma analysis (Ritchie and Nesmith, 1991; Smyth, 2005; Ritchie et al, 2015) was then applied to identify the genes that are differentially expressed at least at one time point with respect to its previous time point (Section Limma Analysis) as described (Schneider et al, 2016). We found that 7376 genes were significantly differentially expressed at least one time point out of a total of 32,836 Arabidopsis genes represented in the data set.…”